Decided to just figure it out, pretty easy job overall. Putting this here in case anyone else is trying to remove the sub and can't find the steps:
1) Pop off the trim that runs along the bottom of the trunk lid, 2 clips if I remember correctly.
2) Pop off the trim at the top of the trunk lid, 5 clips on this one.
3) Pop off the D-pillar trim, 4 clips on here. I found it easiest to pull at the trunk opening and then rotate it forward a little. Because of the seatbelt it won't come all the way off, but sort of hangs out of the way.
4) Pop off the C-pillar trim, 3 clips on here, 1 is above the headliner. It also has 2 grooves that sort of snap onto something behind the trim. I found this also easiest to rotate from the door opening towards the back of the vehicle. Same as the D pillar you can't remove it entirely due to the seat belt, but can hang it out of the way.
5) Remove the piece of trim that covers the jack. 4 x 7mm bolts and lifts out.
6) Remove the piece of trim that runs down the side of the 3rd row seat. A single bolt and then a plastic pin pops up from the storage compartment in the trim.
7) Remove the T50 bolt holding the middle row seat belt.
8) Pull off the trim that runs along the bottom of the rear door. 2 clips on either end and 2 in the middle. Just pulls straight up.
9) You should now be good to pull the panel covering the subwoofer. I forget how many clips it has, 5 or 6 I think, but it pulled off fairly easily.
10) Now you can see the sub enclosure itself. Unplug the amplifier, then remove the 3 x 10mm bolts to remove the enclosure from the vehicle. 1 at the top on each side and one in the middle on the bottom.
11) With the enclosure out of the vehicle, you can then remove the sub. 8 x 6mm bolts on the front and a single one through the back.
Putting it back in again is a reverse of removal. Replaced my sub with a Pioneer TS-SW2002D2, fits perfectly. Funny thing though is my stock sub was apparently fine and the amp was the problem. Followed this fix:
http://www.f150forum.com/f75/how-fix-your-subwoofer-amplifier-7l2t-18c808-aa-227544/ and its working. Decided to keep the Pioneer as it is a nice upgrade though.